An axisymmetric, hydrodynamical model for the torus wind in AGN

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隐式水模型

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Annu.Rev.Phys.Chem.2000.51:129–52Copyright c2000by Annual Reviews.All rights reserved G ENERALIZED B ORN M ODELS OFM ACROMOLECULAR S OLVATION E FFECTSDonald Bashford and David A.CaseDepartment of Molecular Biology,The Scripps Research Institute,La Jolla,California 92037;e-mail:bashford@,case@Key Words solvation energy,continuum dielectricss Abstract It would often be useful in computer simulations to use a simple de-scription of solvation effects,instead of explicitly representing the individual solvent molecules.Continuum dielectric models often work well in describing the thermo-dynamic aspects of aqueous solvation,and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency.Here we give an overview of one such approximation,the generalized Born model,which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids.We discuss its strengths and weaknesses,both for its fidelity to the underlying continuum model and for its ability to replace explicit con-sideration of solvent molecules in macromolecular simulations.We focus particularly on versions of the generalized Born model that have a pair-wise analytical form,and therefore fit most naturally into conventional molecular mechanics calculations.INTRODUCTIONThere are many circumstances in molecular modeling studies where a simplified description of solvent effects has advantages over the explicit modeling of each solvent molecule.One of the most popular models,especially for water,treats the solvent as a high-dielectric continuum,interacting with charges that are em-bedded in solute molecules of lower dielectric.The solute charge distribution,and its response to the reaction field of the solvent dielectric,can be modeled either by quantum mechanics or by partial atomic charges in a molecular me-chanics description.In spite of the severity of the approximation,this model often gives a good account of equilibrium solvation energetics,and it is widely used to estimate pKs,redox potentials,and the electrostatic contributions to molec-ular solvation energies (for recent reviews,see 1–6).For molecules of arbitrary shape,the Poisson-Boltzmann (PB)equations that describe electrostatic interac-tions in a multiple-dielectric environment are typically solved by finite-difference or boundary-element numerical methods (1,7–12).These can be efficiently solved0066-426X/00/1001-0129$14.00129A n n u . 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F o r p e r s o n a l u s e o n l y .130BASHFORD¥CASEfor small molecules but may become quite expensive for proteins or nucleic acids.For example,the DelphiII program,which is a popular program that computes a finite-difference solution,takes about 25min on a 195-Mhz SGI processor to solve problems on a 1853grid with 600atoms.Obtaining derivatives with respect to atomic positions adds to the time and complexity of the calculation (13).Even though progress continues to be made in numerical solutions,and other approaches may be significantly faster,there is a clear interest in exploring more efficient,if approximate,approaches to this problem.One such simplification that has received considerable recent attention is the generalized Born (GB)approach (14,15).In this model,which is derived below,the electrostatic contribution to the free energy of solvation isG pol =−12 1−1w i ,j q i q jf GB , 1.where q i and q j are partial charges,εw is the solvent dielectric constant,andf GB is a function that interpolates between an “effective Born radius”R i ,when the distance r i j between atoms is short,and r i j itself at large distances (15).In the original model,values for R i were determined by a numerical integration proce-dure,but it has recently been shown that “pair-wise”approximations,in which R i is estimated from a sum over atom pairs,can be nearly as accurate and provide a simplified approach to energies and their derivatives (16–21).In the following sections,we present one derivation of this model and compare it to the underlying continuum dielectric model on which it is based.This is followed by a review of pair-wise parameterizations and of practical applications of GB and closely related approximations.Our emphasis is almost exclusively on the use of this approach to describe aqueous solvation of macromolecules.A comprehensive review of other applications of the GB model has recently appeared (6).GENERALIZED BORN AND RELATED APPROXIMATIONSThe underlying physical picture on which the GB approximation is based is the two-dielectric model described above.To obtain the electrostatic potential φin such a model,one should ideally solve the Poisson equation,∇[ε(r )∇φ(r )]=−4πρ(r ),2.where ρis the charge distribution,and the dielectric constant εtakes on the solute molecular dielectric constant εin in the solute interior and the exterior dielectric constant εex elsewhere.For gas phase conditions,εex =1,whereas in solvent conditions,εex =εw ,the dielectric constant of the solvent (here,water);solving Equation 2under these two conditions leads to potentials that can be denoted φsol and φvac ,respectively.The difference between these potentials is the reaction field,φreac =φsol −φvac ,and the electrostatic component of the solvation free energy isG pol =12φreac (r )ρ(r )dV , 3.A n n u . 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F o r p e r s o n a l u s e o n l y .GENERALIZED BORN MODELS 131or if the molecular charge distribution is approximated by a set of partial atomic point charges q i ,G pol =12i q i φreac (r i ). 4.In the case of a simple ion of radius a and charge q ,the potentials can be found analytically and the result is the well-known Born formula (22),G Born =−q 22a 1−1εw. 5.If we imagine a “molecule”consisting of charges q 1···q N embedded in spheres of radii a 1···a N ,and if the separation r i j between any two spheres is sufficiently large in comparison to the radii,then the solvation free energy can be given by a sum of individual Born terms,and pair-wise Coulombic terms:G pol =N i q 2i 2a i 1w −1 +12N i N j =i q i q j r i j 1w −1 , 6.where the factor (1/εw −1)appears in the pair-wise terms because the Coulombicinteractions are rescaled by the change of dielectric constant on going from vacuum to solvent.The goal of GB theory can be thought of as an effort to find a relatively simple analytical formula,resembling Equation 6,which for real molecular geometries will capture,as much as possible,the physics of the Poisson equation.The linearity of the Poisson equation (or the linearized PB equation)assures that G pol will indeed be quadratic in the charges,as both Equations 1and 6assume.However,in calculations of G pol based on direct solution of the Poisson equation,the effect of the dielectric constant is not generally restricted to the form of a prefactor,(1/εw −1),nor is it a general result that the interior dielectric constant,εin ,has no effect.With these caveats in mind,we seek a function f GB ,to be used in Equation 1,such that in the self (i =j )terms,f GB acts as an “effective Born radius,”whereas in the pair-wise terms,f GB becomes an effective interaction distance.The most common form chosen (15)isf GB (r i j )= r 2i j +R i R j exp −r 2i j /4R i R j 12,7.in which the R i are the effective Born radii of the atoms,which generally dependnot only on a i ,the intrinsic atomic radii,but also on the radii and relative positions of all other atoms.Ideally,R i should be chosen so that if one were to solve the Poisson equation for a single charge q i placed at the position of atom i ,and a dielectric boundary determined by all of the molecule’s atoms and their radii,then the self-energy of charge i in its reaction field,q i φreac (r i )/2,would be equal to −(q 2/2R i )(1−1/εw ).Obviously,this procedure per se would have no practical advantage over a direct calculation of G pol using a numerical solution of the Poisson equation.To find a more rapidly calculable approximation for the effective Born radii,we turn to a formulation of electrostatics in terms of integration over energy density.A n n u . 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F o r p e r s o n a l u s e o n l y .132BASHFORD¥CASEDerivation in Terms of Energy DensitiesIn the classical electrostatics of a linearly polarizable media (23),the work required to assemble a charge distribution can be formulated either in terms of a product of the charge distribution with the electric potential,as above,or in terms of the scalar product of the electric field E and the electric displacement D :W =12 ρ(r )φ(r )dV 8.=18π E ·D dV .9.We now introduce the essential approximation used in most forms of GB theory:that the electric displacement is Coulombic in form,and remains so even as the ex-terior dielectric is altered from 1to εw in the solvation process.In other words,the displacement due to the charge of atom i (which for convenience is here presumed to lie on the origin)isD i ≈q i r r3.10.This is called the Coulomb field approximation.In the spherically symmetric case (as in the Born formula),it is exact,but in more complex geometries,there may be substantial deviations,a point to which we turn presently.The work of placing a charge q i at the origin within a molecule whose interior dielectric constant is εin ,surrounded by a medium of dielectric constant εex and in which no other charges have yet been placed,is thenW i =18π (D /ε)·D dV ≈18π in q 2i r 4εin dV +18πex q 2i r 4εex dV .11.The electrostatic component of the solvation energy is found by taking the differ-ence in W i when εex is changed from 1.0to εw ,G pol i =−18π 1−1w ex q ir dV ,12.where the contribution due to the interior region has canceled in the subtraction.1Comparing Equation 12to the Born Formula 5or to Equations 1or 6,we conclude that the effective Born radius should beR −1i =14π ex 1r 4dV .13.1Itmay be noticed that the interior integral contained a singularity at r →0.This a con-sequence of representing the charge distribution as a set of point charges,and similar singularities appear in treatments based on the electrostatic potential.The validity of can-celing out such singularities can be demonstrated by replacement of these point charges by small charged spheres and consideration of the limit as the sphere radii shrink to zero.A n n u . 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F o r p e r s o n a l u s e o n l y .GENERALIZED BORN MODELS 133It is often convenient to rewrite this in terms of an integration over the interior region,excluding a radius a i around the origin,R −1i =a −1i −14π in ,r >a i 1r 4dV ,14.where we have used the fact that the integration of r −4over all space outside radius a is simply 4πa −1.Note that in the case of a monatomic ion,where the molecular boundary is simply the sphere of radius a i ,this equation becomes R i =a i and the Born formula is recovered exactly.The integrals in Equation 13or 14can be calculated numerically by constructing a set of concentric spherical shells around atom i and calculating the fractional area of these shells lying inside or outside the van der Waals volume of the other atoms,j =i (15),or by using a cubic integration lattice (24).Ghosh et al (25)have proposed an alternative approach,in which the Coulomb field is still used in place of the correct field,and Green’s theorem is used to convert the volume integral in Equation 14to a surface integral.At this level,the S-GB (surface-GB)model is formally identical to the model outlined above.(There are potential computational advantages in the surface integral approach,especially for large systems and for evaluating gradients,but these have not yet been exploited.)In practice,empirical short-range and long-range corrections (discussed below)are added to improve agreement with numerical Poisson theory.Solute Dielectrics Other than UnityStrictly speaking,the Coulomb field approximation assures that the internal dielec-tric constant,εin ,does not appear in GB theory;the only dielectric constants that matter are those of the solvent and the vacuum.(See the passage from Equation 11to Equation 12.)However,εin can reappear in an indirect and somewhat deceptive way,in GB-based expressions for energy as a function of solute conformation or intermolecular interaction energies.In such cases,one would like to have a poten-tial of mean force described on the hypersurface of the solute degrees of freedom.Its electrostatic component would bePMF elec =E elec ,ref + G pol (ref →sol ),15.where E elec ,ref is the electrostatic energy of the solute in some reference environ-ment that is chosen so that the calculation can be done simply,and G pol (ref →sol )is the energy of transferring the system from this reference environment to solvent.If the solute is presumed to have an internal dielectric of 1,the obvious choice of reference medium is the vacuum,where E elec ,ref can be calculated by Coulomb’s law,and the usual GB expressions for G pol can be used unchanged for G pol (ref →sol ).However,if the internal dielectric has a value εin that is different from 1,a more convenient choice is a reference medium of dielectric constant εin ,so that Coulomb’s law can again be used.In this case,all occurrencesA n n u . 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F o r p e r s o n a l u s e o n l y .134BASHFORD¥CASEof (1−1/εw )in the GB theory expressions are replaced by (1/εin −1/εw ).The resulting expression for the electrostatic potential of mean force isPMF elec =12 i =j q i q j in r i j −12 i ,j 1in −1wq i q jf GB i j 16.(compare with Equation 1).At long distances,where f GB goes to r i j ,the εin de-pendence disappears.It should be emphasized that εin appears in these formulaenot so much because it is the internal dielectric constant as because it is the ex-ternal dielectric constant of the reference environment.In particular,GB theory,because of its Coulomb field approximation,and in contrast to Poisson-equation theory,cannot capture the tendency of solvation to increase the dipole moment of a dipolar solute,thus enhancing its solubility,through the use of an internal dielectric constant.Of course,such effects can be captured by methods that ex-plicitly couple some other theory of solute polarizability to GB theory,e.g.though quantum mechanical descriptions of the solute (6).Incorporation of Salt EffectsGB models have not traditionally considered salt effects,but the model can be extended to low salt concentrations at the Debye-Huckel level by the following arguments (21).The basic idea of the GB approach can be viewed as an inter-polation formula between analytical solutions for a single sphere and for widely separated spheres.For the latter,the solvation contribution in the Poisson model becomesG pol =− 1−e −κr i j wq i q jr i j ,17.where κis the Debye-H¨u ckel screening parameter.The first term removes the gas-phase interaction energy,and the second term replaces it with a screened Coulombpotential.For a single spherical ion,the result is (26,27)G pol =−12 1−1εwq 2a −q 2κ2εw (1+κb ),18.where a is the radius of the sphere and b is the radial distance to which salt ionsare excluded,so that b −a is the ion-exclusion radius.To a close extent,these two limits can be obtained by the simple substitution1−1w → 1−e −κf GBw19.in Equation 1.This reduces directly to Equation 17for large distances,and thesalt-dependent terms become,as r i j goes to zero,−q 2i κ2εw 1+12κR i 20.A n n u . 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F o r p e r s o n a l u s e o n l y .GENERALIZED BORN MODELS 135through terms in κ2.To terms linear in κ,Equations 20and 18agree,but the quadratic terms differ by the replacement of b with 1/2(R i ).In practice,Equation 19gives salt effects that are slightly larger than those predicted by finite-difference linearized PB calculations,but which are strongly correlated with them.One likely reason is that the GB model outlined here does not have the concept of an ion-exclusion radius and,hence,tends to overestimate salt effects (compared with the usual PB model)by allowing counterions to approach more closely to the solute than they should.A simple ad hoc modification that leads to acceptable results can be obtained by a simple scaling of κby 0.73in Equation 19(21).Figure 1compares linearized PB and GB estimates of the effect of monovalent added salt on the solvation energy of a 10-bp DNA duplex.The GB model is clearly capturing most of the behavior of linearized PB,especially at low salt concentrations.It is worth emphasizing that the linearized PB model itself is an imperfect model for salt effects (28),so that Equation 20should only be viewed as a rough approximation;it does,nonetheless,introduce the exponential screening of long-range Coulomb interactions,which is one of the hallmarks of salt effects.Limitations and Variations of the GB ModelThe crux of the GB approximation for the self-energy terms and effective radii is the Coulomb field approximation,Equation 10,and this is also the main source of its deviation from solvation energies calculated using solutions of thePoissonFigure 1Difference in the solvation energy at finite and zero added salt for a 10-bp DNA duplex,calculated by numerical solutions to the linearized PB model,and from Equation 38.(Data from Reference 21.)A n n u . 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F o r p e r s o n a l u s e o n l y .136BASHFORD¥CASEequation.In general,the electric displacement generated by a charge q i located at a position r i within the low dielectric cavity of the solute will consist of a Coulomb field and a reaction field component D reac ,the latter being a consequence of the nonuniformity of the dielectric environment.The reaction field contains no Coulombic singularities within the molecular interior and is usually fairly smoothly varying within this region.If the dielectric boundary between solvent and solute is sharp,which is the usual assumption,then D reac can be thought of as arising from an induced surface charge density on the dielectric boundary.In spherically symmetric cases,such as the case analyzed in the original Born theory,D is given exactly by the Coulomb field (D reac is zero),and GB solvation goes over into Poisson-equation solvation.Schaefer &Froemmel (29)have an-alyzed deviations from the Coulomb-field approximation for the case of charges at arbitrary positions within a spherical dielectric boundary,a case for which an-alytical solutions of the Poisson equation are available (26).They found that the Coulomb field approximation leads to significant errors in both self-energies and in the screening of charge-charge interactions,and they proposed an image-charge approximation for D reac that is very successful in recovering the energetic behavior of the exact Poisson model.Some additional quantitative sense of the limitations of the Coulomb field ap-proximation can be gained by considering the case of a charge near a planar dielectric boundary (Figure 2).This can be thought of as the infinite-radius limit of the situation where a charge is a distance d below the surface of a spherical macromolecule with a large radius (R d )and a dielectric constant εin ,and the macromolecule is transferred from an external medium of dielectric constant εin to a medium of dielectric constant εw .The electrostatic potential can be found exactly by the method of images (23).φz >0=q εin r 1+q εin r 2φz <0=q ex r 1,21.whereq =−qεex −εin ex in q =q 2εexex in .22.The reaction field in the z >0region corresponding to a change of εex from εin to εw isφreac =q εin r 2=−q εw −εin εw +εin1εin r 2,23.A n n u . 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F o r p e r s o n a l u s e o n l y .GENERALIZED BORN MODELS137Figure 2A point charge q near a dielectric interface at z =0.The dielectric constant is εin or εex in the positive or negative z regions,respectively.The potential on the +z side is a sum of the Coulomb potential of the real charge q at z =d ,and an image charge q at z =−d .The potential on the −z side is the Coulomb potential of an image charge q at z =d .The distances of an arbitrary point r from the z =d and z =−d charge locations are denoted as r 1and r 2,respectively.where the r 1term has canceled in the subtraction of the potential in the εex =εin case from the potential in the εex =εw case.The electrostatic solvation energy can be found using Equation 4,G pol (exact )=−q 24d εw −εin εin (εw +εin )=−q 24d 1εin −1εw11+εin /εw .24.The corresponding formula for the solvation energy according to the Coulomb-field approximation and an integration of the energy density difference over the“exterior”(z <0)region can be obtained using Equation 12:G pol (Coulomb )= 1in −1w 18πz <0q 2r 2=−q 28d 1in −1w .25.Note that in the usual case where εw εin ,the magnitude of G pol is underesti-mated by a factor of almost 2compared with the exact expression,Equation 24,although the form of the dielectric-constant dependence,a factor of (1/εin −1/εw ),is approximately correct.This suggests that for charges buried somewhat below the surface of large macromolecules,the |W i |of Equation 11may be underestimated,and thus the effective Born radii overestimated because of the Coulomb-field ap-proximation.Of course the methods of approximating density integrals (such asA n n u . 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F o r p e r s o n a l u s e o n l y .138BASHFORD¥CASEthe pair-wise descreening approximation decribed below)will also affect the re-sults.On the other hand,most of the solvation energy of a macromolecule will be due to charged or highly polar groups that protrude into solvent,and for these groups,GB theory may be expected to work nearly as well as for analogous groups in small molecules.Luo et al (30)have also examined errors arising from replacing the true field with a Coulomb approximation.Essentially,they assume that E ≈E vac /d F ,where E vac is the vacuum Coulomb field and d F is a screening parameter having different values in the interior region or exterior regions.In the centrosymmetric case,d F is identical to the dielectric constant,but for more general shapes,it is a parameter to be optimized to provide realistic solvation energies.This leads toG pol =−18πεw −1d Fex E 2vac dV .26.Noting that in the Coulomb field approximation D =E vac ,this expression is similarto Equation 12with (1−1/εw )replaced by (εw −1)/d F .Its other difference from GB theory is that this expression is used for the entire solvation energy,implicitly including charge-charge interactions terms rather than using a formula such as Equation 7.On a number of test cases,it was found to give good agreement with Poisson calculations,but the numerical integration required had roughly the same computational cost as solving the Poisson equation numerically.The limitations of both the density integration methods and the Coulomb field approximation are also addressed in the electrostatic component of the SEED method for docking small molecular fragments to a macromolecular receptor (31).The desolvation of the receptor by the low dielectric of the ligand is taken to be the integral of D 2/(8π)over the ligand volume,and D is assumed not to change on ligand binding,as in conventional GB theory.The integration is done numerically using a cubic lattice,and the user can choose whether to estimate D by the Coulomb field approximation,as in GB theory,or to calculate it by a finite difference solution of the Poisson equation for the ligand-free receptor.In its use of a D obtained by solving the Poisson equation,this method is similar in spirit to the SEDO approximation described below,except that the latter is based on solvation energy density rather than D 2.Solvation Energy DensityIn Equation 12,the solvation energy is expressed as the volume integral of an energy density that is zero within the solute volume,so that the integral need only run over the solvent volume.This could be thought of as a solvation energy density,but it is only by virtue of the Coulomb field approximation that it falls to zero in the solute region.It is possible to give a more rigorous definition of solvation energy density that does not depend on approximations (32).In classical continuum electrostatics,an important problem is to find the energy change caused by placing a dielectricA n n u . 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F o r p e r s o n a l u s e o n l y .object within some volume,in the electric field of a fixed set of charges outside that volume.This is essentially the same as the present solvation problem:We seek the change of energy associated with changing the dielectric constant of the region outside the molecule V ex ,from εvac to εw ,in the presence of the atomic partial charges,which remain fixed in the molecular interior.Denoting the electric field and displacement before the dielectric alteration as E vac and D vac ,and after the alteration as E sol and D sol ,respectively,the energy change isG pol =18π (E sol ·D sol −E vac ·D vac )dV ,27.where the volume integration runs over all space.It can be shown (23)that Equation 27can be transformed intoG pol =18π (E sol ·D vac −D sol ·E vac )dV ing D =εE ,it can be seen that the integrand falls to zero in the molecular interior because the dielectric constant there does not change (i.e.E sol ·εin E vac −εin E sol ·E vac =0).One can then writeG pol =exS (r )dV ,29.where the integral runs only over the exterior region,and S is the solvation energydensity,defined byS =18π(E sol ·D vac −D sol ·E vac ).30.No approximations have been introduced up until this point,and Equations 29and 30are fully equivalent to Equation 3.Of course,if one introduces the Coulomb field approximation,Equation 10,into the expression for S ,the GB theory expression for self energies is obtained.A different approximation based on S and oriented toward estimating desol-vation effects in intermolecular interactions has recently been proposed by Arora &Bashford (32).Suppose one would like to calculate the effect of the approach of a second molecule on the solvation energy of the first molecule.The effect of the low dielectric of the second molecule on the solvation energy density S of the first is twofold.First,S will go to zero in the interior of the second molecule,in other words a portion of S will be occluded.Second,in the solvent region near the second molecule,there will be some rearrangement of S .The approximation is to include the first effect but neglect the second.This means that one can precalculate S by solving the Poisson equation and differentiating the potential to obtain the field and displacement in both vacuum and solvent,for the first molecule alone.Then the desolvation effect of a second molecule can be obtained byG desol =−mol 2S mol 1dV .31.A n n u . 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河流动力学英语

河流动力学英语

水力学、河流动力学、流体力学专业词汇Fundamental Glossary in HydraulicsHydrostatics 水静力学Hydrodynamics 水动力学Physical properties of water 水的物理性质Density 密度Specific gravity 比重Kinematic viscosity 运动粘性Absolute viscosity 动力粘性Elastic modulus 弹性模量Surface tension 表面张力Temperature 温度Isotropic (y) 各向同性Anisotropic (y) 各向异性Uniform (ity) 均匀(性) Heterogeneous (ity) 不均匀(性)Main force 主要作用力Gravity 重力Inertia force 惯性力pressure 压力(强)Drag 阻力Mass force 质量力Surface force 表面力Constitutive relationship 本构关系Stress 应力Strain 应变Deformation 变形Displacement 位移Normal 法向Tangent 切向Shear 剪力Acceleration 加速度Angular deformation 角变形Local acceleration 当地加速度convective acceleration 迁移加速度compressibility 压缩性continuity连续性Scalar 纯量vector 矢量tensor 张量magnitude 模(大小) direction 方向Divergence 散度curl 旋度gradient 梯度Source 源sink 汇Frequency 频率amplitude 振幅phase 相位resonance共振Mass conservation 质量守恒momentum conservation 动量守恒energy conservation 能量守恒Initial condition 初始条件boundary condition边界条件Ordinal differential equation 常微分方程partial differential equation 偏微分方程Convection, advection 对流diffusion 扩散dispersion 弥散decay 衰减degradation降解Flow pattern流态flow type 流型Laminar flow 层流turbulent flow 紊流Supercritical flow 急流subcritical flow 缓流critical flow临界流Rapidly varied flow急变流gradually varied flow渐变流Uniform flow 均匀流non-uniform flow 非均匀流Mainstream flow 主流wake flow 尾流Steady flow 恒定流unsteady flow 非恒定流One-dimensional flow 一维流two-dimensional flow二维流three-dimensional flow 三维流Single-phase flow 单相流double-phase flow 两相流multi-phase flow 多相流Irrotational flow 无旋流potential flow 势流rotational flow 有旋流Open channel flow 明渠流free surface flow 自由表面流(明渠流)Pipe flow 管流pressure flow 有压流Jet 射流plume 卷流(羽流) cross flow 横流Stagnation point驻点separation point分离点Coherent structure相干结构bursting猝发turbulent intensity紊动强度Boundary layer 边界层viscous sub-layer粘性底层displacement thickness排挤厚度mixing length混掺长度Flow field, current field 流场flow net 流网Submerged discharge 淹没出流unsubmerged discharge非淹没出流Renolds number雷诺数Froude number 佛汝德数Prandtl number普朗特数Courant number柯朗数Peclet 彼克雷特数dimensionless number无量纲数Streamline 流线path line迹线Vortex line 涡线vortex ring 涡环vortex street涡街Flux 通量circulation 环量vorticity 涡度Water level , water stage 水位discharge , flow-rate , flow 流量Water depth 水深velocity 流速Roughness 糙率water surface profile 水面线bed slope 底坡Velocity fluctuation 脉动流速pressure fluctuation 脉动压强Instantaneous velocity 瞬时流速mean velocity 平均流速time-averaged velocity时均流速Depth-averaged velocity 水深平均流速velocity gradient 流速梯度pressure gradient压强梯度Cross-section of flow , wet cross section 过水断面Wetted perimeter 湿周hydraulic radius水力半径Hydraulic head 水头Elevation head 位置水头piezometric head测压管水头velocity head 流速水头Head loss水头损失frictional loss 沿程损失local head loss局部损失Entrance head loss 进口水头损失exit head loss 出口水头损失bend head loss弯头水头损失Abrupt expansion head loss 突扩损失contraction head loss收缩损失Transition head loss渐变段损失Hydraulic jump 水跃hydraulic drop跌水conjugate depth共轭水深Weir堰Sharp-crested weir 尖顶堰broad-crested weir 宽顶堰practical weir实用堰Orifice 孔口nozzle管嘴Dam 坝sluice 水闸spillway溢洪道Tunnel 隧洞penstock 压力水管culvert涵洞Aqueduct 渡槽siphon pipe虹吸管Energy dissipation device 消能工Stilling basin 消力池roller bucket 消力戽Baffle pier 消力墩plunge pool 跌水池Energy dissipation by hydraulic jump底流消能Energy dissipation by surface regime面流消能Ski-jump energy dissipation 挑流消能Nappe 水舌vena-contracta收缩断面Cavitation 空化cavitation damage 空蚀Aeration 掺气Water wave 水波water hammer水锤Hydraulic and river dynamics 水力学及河流动力学Sediment 泥沙bed load 床沙suspension load 悬沙wash load 冲泻质Incipient velocity起动流速settling velocity沉速Fluvial process河床演变de">Grounder water 地下水seepage渗透permeability 渗透性Similarity[simi’l&aelig;riti] theory 相似理论Hydraulic modeling水力模拟Physical modeling 物理模拟Undistorted model正态模型distorted model变态模型Similitude 相似准则similarity 相似性full scale 足尺reduced scale缩尺Fluid measurement 流动量测flow visualization 流动可视化Transducer,sensor 传感器probe探头scale 比尺flume 水槽Numerical modeling数值模拟Finite element 有限元finite difference有限差finite volume 有限体积boundary element边界元Characteristics 特征线Scheme 方法(格式) algorithm 算法turbulence model 紊流模型Large-eddy simulation 大涡模拟Grid 网格node结点time step时间步长nodal spacing 结点间距Coefficient系数parameter参数Explicit 显式implicit隐式stability 稳定性convergence收敛性robustness(坚固性)健壮性sensitivity 敏感性accuracy 精度Error误差calibration 率定verification 验证application 应用prediction 预测reproduction复演Estuary hydraulics 河口动力学Coastal hydraulics 海岸动力学Open channel hydraulics明渠水力学Wave hydrodynamics 水波动力学Groundwater Hydraulics地下水水力学regular wave 规则波irregular wave 不规则波Tide潮汐spring tide大潮neap tide小潮diurnal tide全日潮semi-diurnal tide半日潮Computational Hydraulics计算水力学Environmental Hydraulics环境水力学Eco-hydraulics 生态水力学Hydro-informatics 水利信息学Dissolved oxygen (DO) 溶解氧chemical oxygen demand(COD) 化学需氧量Biochemical oxygen demand(BOD) 生化需氧量dilution 稀释度Pollutant 污染物constituent 组分eutrophication 富营养化Hydrology水文学Flood洪水flood routing调洪演算flood peak flow洪峰流量Runoff径流precipitation降水evaporation蒸发evapotranspiration 腾发, 蒸散发。

涉及非体积功的热力学基本方程

涉及非体积功的热力学基本方程

第49卷第8期2021年4月广州化工Guangzhou Chemical IndustryVol.49No.8Apr.2021涉及非体积功的热力学基本方程杨嫣,陈山川,谢娟,张改(西安工业大学材料与化工学院,陕西西安710021)摘要:热力学基本方程是物理化学课程中一个重要的知识点。

现行物理化学教材中重点阐述了仅含有体积功的热力学基本方程,而对涉及非体积功的热力学基本方程介绍很少。

对材料类专业的学生来说,学习和研究材料热力学,经常会涉及到非体积功。

因此,学习涉及非体积功的热力学基本方程非常必要。

本文重点讨论了涉及非体积功的表面系统、弹性杆、电、磁介质中的热力学基本方程的推导和应用,并总结了处理这类问题的方法。

关键词:物理化学;热力学;基本方程;非体积功中图分类号:G642文献标志码:A文章编号:1001-9677(2021)08-0139-04 Fundamental Equations in Thermodynamics Involving Non-expansion Work*YANG Yan,CHEN Shan-chuan,XIE Juan,ZHANG Gai(School of Material Science and Chemical Engineering,Xi9an Technological University,Shaanxi Xi'an710021,China) Abstract:Fundamental equation in thermodynamics is one of the key points of Physical Chemistry course・In current Physical Chemistry textbooks,the fundamental equations containing only expansionwork are mainly described, while the ones involving non-expansionwork are rarely introduced.For the students majoring in materials,non-expansionwork is often involved in the processes of studyand research.Therefore,it is necessary to study the fundamental equations in involving non-expansion work.The derivations and applications of the fundamental equations in surface systems,elastic rods,electric and magnetic media were discussed.Moreover,the way to deal with this kind of problem was summarized.Key words:Physical Chemistry;thermodynamics;the fundamental equation;non-expansion work热力学基本方程在处理平衡态热力学问题时非常有用,是物理化学课程内容的重点之一。

求解半无限长多孔介质柱体水动力弥散系数的一种最小二乘法

求解半无限长多孔介质柱体水动力弥散系数的一种最小二乘法

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hydrodynamicprediction method -回复

hydrodynamicprediction method -回复

hydrodynamicprediction method -回复什么是水力动力学预测方法?在当今工程和科学领域中,水力动力学预测方法是一个重要的工具,用于研究和预测液体在流动中的行为和性质。

无论是在水力建筑设计,河流管理,或是海洋工程等领域,水力动力学预测方法都是不可或缺的。

水力动力学预测方法的原理是基于数学和物理模型的建立。

这些模型通过对流体力学和运动学的原理进行数学描述,以实现对流体行为的模拟和预测。

这些模型可以用于分析和预测各种液体流动的参数,如流速、压力、液体界面等。

在水力动力学预测方法中,最常用的是数值模拟方法,包括有限元方法和有限差分方法。

这些方法通过将流体领域划分为离散的网格点,然后建立将流体行为描述为一组非线性方程的数学模型。

然后利用数值计算技术求解这些方程,以得到流体的各种参数。

这些方法能够模拟各种复杂的流体现象,如液体的湍流、分离流、涡流等。

水力动力学预测方法的应用非常广泛。

在水力建筑设计中,可以用于研究和预测水坝的流量分布、压力分布等参数,以保证大坝的安全性。

在河流管理中,水力动力学预测方法可以用于模拟河流中的液体流动,以研究河流的侵蚀和沉积规律,从而为河道疏浚和河岸保护提供依据。

在海洋工程中,水力动力学预测方法可以用于预测海洋中的潮汐、风浪等参数,从而为海上建筑物和船只的设计提供基础。

然而,水力动力学预测方法也存在一些挑战和限制。

首先,数值模拟方法的计算量较大,需要大量的计算资源和时间。

其次,在复杂的流体现象中,模型的建立和参数的确定也是非常困难和复杂的。

此外,模型的假设和误差也会对预测结果产生影响。

因此,在应用水力动力学预测方法时,需要谨慎选择合适的模型,并根据实际情况进行修正和验证。

综上所述,水力动力学预测方法是一种重要的工具,用于研究和预测液体在流动中的行为和性质。

通过建立数学和物理模型,并运用数值模拟方法,可以模拟和预测各种复杂的流体现象。

然而,在应用水力动力学预测方法时,需要注意模型选择和参数校验,以保证预测结果的准确性和可靠性。

面元法与鱼尾摆动的三维非定常流动物理研究的开题报告

面元法与鱼尾摆动的三维非定常流动物理研究的开题报告

面元法与鱼尾摆动的三维非定常流动物理研究的开题报告一、研究背景与意义面元法和鱼尾摆动是非定常流动研究中重要的研究方向,有着广泛的应用前景。

面元法是一种利用流体表面表示非定常流动运动的方法,适用于研究小振幅振动、非对称流动及复杂结构运动的流体动力学问题。

而鱼尾摆动则是流体动力学中的一个重要现象,在海洋工程、生物力学、船舶工程等领域有着广泛的应用。

本次研究旨在通过数值模拟的方法,研究面元法和鱼尾摆动的三维非定常流动物理现象,通过对流场、压力场的分析和计算,探究流动的规律,为这些问题的进一步研究提供理论基础和实际应用的指导。

二、研究内容与方法1. 研究内容(1)面元法在三维非定常流动中的应用研究;(2)鱼尾摆动的三维非定常流动数值模拟研究;(3)流场、压力场的分析和计算;(4)对流动规律的分析和探究。

2. 研究方法(1)利用数学模型和计算流体力学(CFD)技术对问题进行数值模拟分析,得到流场和压力场的数据;(2)采用可视化技术和统计分析方法对数据进行处理和分析,探究流动的规律;(3)结合现有理论和实验数据进行验证和对比,进一步深入探究面元法和鱼尾摆动的物理本质。

三、预期成果(1)获得面元法和鱼尾摆动的三维非定常流动的流场和压力场相关数据;(2)深入了解面元法和鱼尾摆动的物理本质,并探究其流动规律;(3)提高面元法和鱼尾摆动等问题的数值模拟分析能力,为相关领域的进一步研究提供理论基础和实际应用的指导。

四、进度安排阶段一:调研文献,研究数值模拟和可视化技术。

时间:1个月。

阶段二:建立数学模型,进行数值模拟和数据处理。

时间:3个月。

阶段三:分析数据,探究流动规律,撰写论文。

时间:2个月。

阶段四:完成论文的修改和整理,准备答辩。

时间:1个月。

预计在6个月内完成研究任务。

新安江模型与水动力学模型结合修正研究

新安江模型与水动力学模型结合修正研究

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板结构特性分析

板结构特性分析
23
實驗力學研究室
Beam Coordinate System
24
實驗力學研究室
25
實驗力學研究室
Stress Recovery in Beams
Tensile and compressive stress is calculated for the entire beam, but reported bending stress and stress from torsion will depend on your choice of stress recovery points.
3Dsimulation and modeling
• Beam simulation • Symmetry or anti-symmetry • Plate or shell models • Solid models
2
實驗力學研究室
Plane Stress Modeling
The definition of plane stress requires that the behavior of interest occurs in such a manner that there is no stress component normal to the plane of action. This means that one of the three principal stresses is zero.
18

實驗力學研究室
Cyclic Symmetry
Cyclic symmetry is a more specialized condition where features that are repeated about an axis can be modeled by a single instance of that feature.
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An axisymmetric,hydrodynamical model for the torus wind inAGN.A.Dorodnitsyn 1,2,T.Kallman 1,and D.Proga 3ABSTRACTWe report on time-dependent axisymmetric simulations of an X-ray excited flow from a parsec-scale,rotating,cold torus around an active galactic nucleus.Our simulations account for radiative heating and cooling and radiation pressure force.The simulations follow the development of a broad bi-conical outflow induced mainly by X-ray heating.We compute synthetic spectra predicted by our simulations.The wind characteristics and the spectra support the hypothesis that a rotationally supported torus can serve as the source of a wind which is responsible for the warm absorber gas observed in the X-ray spectra of many Seyfert galaxies.Subject headings:acceleration of particles –galaxies:active –hydrodynamics –methods:numerical –quasars:absorption lines –X-rays:galaxies 1.Introduction Approximately 50%of low-red-shift AGNs exhibit spectra rich in atomic absorption features in the X-ray band.These spectra,referred to as warm absorbers,contain numerous lines and bound-free edges from ions of intermediate-Z elements,and indicate blue-shifts of the absorbing material of 102−103km s −1.The term refers to the fact that the X-ray absorbing gas has an electron temperature and ionization degree which are interme-diate between that expected for neutral and fully ionized material.Warm absorber gas has been known for more than two decades,beginning with observations using the Einstein Ob-servatory satellite (Halpern 1984),although the limited spectral resolution of early X-ray experiments hampered a detailed study of its properties.1Laboratory for High Energy Astrophysics,NASA Goddard Space Flight Center,Code 662,Greenbelt,MD,20771,USA2Space Research Institute,Profsoyuznaya st.,84/32,117997,Moscow,Russia 3Department of Physics and Astronomy,University of Nevada,Las Vegas,NV 89154,USAa r X i v :0801.1470v 1 [a s t r o -p h ] 9 J a n 2008Recent X-ray telescopes,Chandra and XMM-Newton,provide unprecedented spectral resolution up to∼10keV,and have revealed much of the complexity of warm absorber spectra.The ubiquity of X-ray warm absorbers and the implication of outflow in objects which are likely powered by accretion,combine to make warm absorbers of great interest for the understanding of active galactic nuclei.While observationally the reality of the X-ray absorbing gas isfirmly established,the source of this gas remains uncertain.If the wind originates from an accretion disk(Konigl&Kartje1994;Murray et al.1995),then warm absorber gas can occupy a vast spa-tial region from the inner accretion disk up to and beyond the broad line region.In addition, it is likely to have a speed which is comparable to the escape velocity in the region where the wind originates.If so,the line widths favor a wind originating far outside the inner accretion disk,at∼1pc,for an AGN containing a106M black hole.The natural source of gas at this distance is the molecular torus which is responsible for obscuring the broad line region in Seyfert2galaxies,and which is thought to exist in some form in many low and intermediate luminosity AGN(Antonucci&Miller1986). The existence of an outflow from the torus has been suggested by(Krolik&Begelman1986; Krolik&Begelman1988),and as the source of warm absorberflows by(Krolik&Kriss1995; Krolik&Kriss2001).Direct interferometric observations of this dusty structure have recently become avail-able:mid-infrared high spatial resolution studies of the active nucleus of NGC1068,revealed a dust torus-like structure that is2.1pc thick and3.4pc in diameter(Jaffe et al.2004). Evidence of at least two temperature components has been established:thefirst one is ex-tended and warm(320K)and conceals the second,which is compact and hot(>800K).It is natural to assume that the latter component can be attributed to the inner part of the torus,heated by the radiation from the compact nucleus.Although such evidence is most solid for nearby active galaxies it is likely that the same obscuring torus paradigm may ap-ply in quasars whose central regions are heavily obscured by gas and dust(Type II quasars) (Zakamska et al.2006).The work done so far in modeling torus warm absorberflows employ either one-dimensional models e.g.(Chelouche&Netzer2005)or two dimensional models which omit rotational forces and also employ an artificial shape for the torus,which is adopted as a boundary for theflow(Balsara&Krolik1992).These calculations support the idea that the outflow originates at r∼1pc-the estimate supported both from virial arguments and also deduced from the warm absorber line widths.The content of the warm absorber gas is highly ionized cosmically abundant heavy elements.This gas can occupy a region from0.01pc to∼10pc from the nucleus.The column densities are in the range1021−1024cm−2.These estimatesare consistent with constraints on the position of the warm absorber gas,which are deduced from the absence of correlated variability of the line equivalent widths to changes of the continuum (Netzter et al.2003;Behar et al.2003).The goal of the current work is to show that a state-of-the-art hydrodynamic model of the evaporative torus wind possesses key characteristics of the the warm absorber.To approach this goal,in this paper we present results of models containing the following in-gredients:1)Time-dependent axisymmentric numerical simulations that take into account rotational forces ,X-ray heating and cooling and radiation pressure both in spectral lines and continuum;2)Exploration of the resulting distributions of density,velocity etc.;and3)A calculation of the synthetic X-ray absorption spectra using the density and velocity distributions as input.Although calculating the spectra is crucial to check the relevance of the particular hydrodynamic solution to the warm absorber phenomenon,the primary goal of the work reported here is the outflow dynamics .2.Basic equationsThe equations to be solved include:∂ρ∂t +∇·(ρv )=0,(1)ρ ∂v ∂t+(v ·∇)v =−∇p −ρ∇Φ+ρg rad ,(2)∂ ∂t +∇·(v ( +p +ρΦ))=H ,(3)these are the conservation equations for:mass,momentum and energy.Heating and cooling processes are described by the function H (erg cm −3s −1); -is the sum of the kinetic and internal energy densities: =ρv 2/2+e .Three components of the velocity are taken into account.However,the adopted azimuthal symmetry implies that all ∂/∂φ=0.The gas is assumed to have a constant adiabatic index,so that e =P/(γ−1)with γ=5/3.Equations (1)-(3)are cast in a non -dimensional form with the characteristic scales set by the properties of the plasma orbiting at a distance of R 0=1pc from a black hole with massM 6in units of 106M :time in measured units of t 0(s)=4.7·1011r 3/2pc M −1/26,velocity inunits of V 0(cm s −1)=6.6·106M 1/26r −1/2pc .We anticipate that the conditions at the interface of a torus and an outflow driven by X-ray heating will resemble the X-ray self-excited wind in X-ray binaries.That is,an X-rayheated skin is created at the outer layers of the companion star atmosphere as a result of X-ray heating by the compact object.The temperature there rises almost discontinuously to some value that allows the gas to escape the gravity of the star.Theflow below the jump is subsonic and is determined by the details of the heating,cooling,and transfer processes in this region(Basko et al.1977).In such a situation,the distribution of temperature depends on the heating and cooling,including both adiabatic effects and radiation,in the equations of hydrodynamics.This can only be calculated accurately if the interior of the star is included as part of the computational domain,and the same applies to the problem of interest to us: the torus X-ray excited wind.We,therefore include in our computational domain the entire volume containing the torus and we start our simulations from a rotating torus configuration in equilibrium in the external gravitationalfield of the black hole.A stationary,polytropic,toroidal structure with constant angular momentum was sug-gested by(Papaloizou&Pringle1984)(PP-torus),and was shown to be stable in2.5di-mensions against radial or axial perturbations,an found to be unstable to non-axisymmetric perturbations(this effect cannot be numerically investigated in axisymmetry).In our dimen-sionless units the locus of the maximum torus densityρmax occurs at R0,so thatρmax=1. The distortion of the torus is controlled by the parameter d=( ++ −)/(2R0),where ±refers to the inner or outer edge of the torus.No replenishing of the torus gas is assumed, i.e.gas can only leave computational domain.The drawback of this approach is that it is not possible to obtain a true stationary solution of the problem.Nonetheless,as we will show,the torusflow can be regarded as a quasi-equlibrium on timescales shorter than the depletion timescale,and can thus provide representative snapshots of the character of the flow.2.1.X-ray exited wind:evolution of the wind and the torusThe thermodynamic properties of X-ray heated gas depend on the spectrum of the incident radiation as well as on the local atomic physics.Under the assumption of photo-ionization equilibrium the thermodynamic state of the gas can be parameterized in terms of ratio of radiation energy density to baryon density(Tarter,Tucker,&Salpeter1969):ξ=4πF x/n,where F x=L x e−τ/(4πr2)is the local X-rayflux,L x is the X-ray luminosity ofthe nuclei,τ=r0κeρdr-is the optical depth.We assume that the attenuation is dominatedby Thomson scatteringκ=0.2(1+X H) 0.4cm2g−1,where X H is the mass fraction of hy-drogen,and the factor e−τ-describes approximately the attenuation of the radiation on the way from the source toward afiducial point.Assuming that the there is a fractionηx of the total luminosity L BH available in X-rays and that the disk radiates a fractionηedd of its Ed-dington luminosity L edd =1.25·1044M 6we estimate:ξ 4·102·ηx ηedd M 6/(N 23r pc ),where r pc -is the distance in parcecs and N 23is the column density in 1023cm −2.If the wind is driven by thermal evaporative mechanism,then its pressure and temperature are determined by the condition of photo-ionization equilibrium,if the dynamical time within the flow is much larger than the characteristic time of the heating-cooling.In a stationary flow the rate of the Comp-ton and photo-ionization heating should be balanced by the Compton,radiative recombina-tion,bremsstrahlung and line cooling respectively.In the calculations we adopt approximate formulas of (Blondin 1994)for these processes.The radiative acceleration,g rad ,accounts for both the acceleration due to lines g rad =(F UV κ/c )k t −α (1+τmax )(1−α)−1 /τ1−αmax ,where L UV is the UV flux,t =σe v th ρ/|dv/dr |,v th is the thermal velocity,σe is the electron-scattering opacity,and α=0.5(Castor,Abbott,&Klein 1975;Stevens &Kallman 1990),and for radiation pressure on electrons g cont =F UV κ/c .In our approach,the radiation force which is due to lines and also k and τmax depend on the ionization parameter ξ,and we adopt the description made by (Stevens &Kallman 1990).The ionization parameter ξis calculated self-consistently at each grid zone,at each time step taking into account the attenuation of the X-ray flux due to finite radial optical depth.We adopt spherical-polar (r,θ,φ)coordinates for calculation of a wind heated by a central source of radiation.We extend the computational domain r i from r in =0.01pc to r out =50pc and the polar domain θi from 0to πwith no assumption about the equatorial symmetry.Models presented here have been calculated with a N r ×N θ=100×100grid.We have also performed test calculations on the 300×300grid finding no noticeable difference with the result presented here.We postpone the discussion of this and related issues to a separate publication.Both angle and radial grids are non-uniformly spaced:the angle gradually increases towards θ=π/4with fewer angular points towards the pole (θ=0)and equator (θ=π/2),and analogously spaced in the southern hemisphere.The use of a logarithmically spaced radial grid allows for the ”throat”of the torus to be resolved.We set outflowing boundary conditions at both ends of the radial grid and axially symmetric at θ=0,π.This initial torus is imbedded in a low density gas with ρ=10−4ρmax ,where ρmax is the maximum density inside the initial torus.To solve the hydrodynamical part of the system of equations (1)-(3)we use the ZEUS-2D code described by (Stone &Norman 1992).As a test we have evolved a torus distribution of matter for t =2(two rotational periods in our units)and found the whole configuration stable.We include the heating term into the hydrodynamical equations using a fully implicit approach because the characteristic heating time scale can be much shorter than the dynamical time.We assume M 6=1,ηedd =0.4,ηx =0.5and also that 0.5L BH is radiated in UV and contributes to the flow energetics through the radiation force g rad .The initial torus config-uration chosen here is only mildly distorted,the distortion parameter:d =1.25.Following(Papaloizou&Pringle1984),we assume that the distribution of specific angular momentum inside the initial torus,is constant.To ensure that our initial torus is in equilibrium,we follow(Papaloizou&Pringle1984)with the exception that we reduce the effective gravity GM BH/r2(1−ηedd)due to the effect of the radiation pressure.However the real continuum radiation pressure,which is adopted in the calculations,is a factor of e−τr less because of the optical depth effect.Our initial torus is Thomson thickτr( +,θ=π/2) 4.35.Although the torus itself is not the primary topic of this study,the X-ray illumination does affect the interior and average properties of the torus.During the evolution the locus of the maximum torus density(located initially at =1)shifts towards larger .This happens primarily because of the over-pressured region created by the evaporating gas and also because of radiation pressure.This allows for the energy to be deposited directly to the torus interior. In our case,direct radiative heating produces gradients of gas pressure in the torus interior. Thus,by making the initial torus marginally optically thick,we crudely mimic the model in which the torus is sustained against vertical collapse by the gradients of infrared radiation energy density(Krolik2007).In what follows,we describe the torus outflow behavior at three different times after the initial turn-on of X-rays.After one orbital period,an over-pressured region extends to r 4pc throughout the area that is not shadowed by the high density torus.At this time the non-shadowed area lies atθ<56◦.In this space,an axisymmetric region exists between0.7pc< <2.5pc and z<7where the temperature is everywhere,of the order of the local virial temperature (except in the torus interior):T 5T vir(r).Closer to the black hole,the heating is much stronger,leading to T∼107K.High temperature,low density gasfills the space in the ”throat”of the torus.The outer edge of the torus has extends to∼5.3pc in temperature, and to∼4.5pc in density contours.The ionization parameter in the same region isξ 600.A wind is well-developed:the velocityfield in the vicinity of the high density torus,follows the equal pressure contours;the maximum radial velocity is observed close to the axes at v max(θ=3◦)=1180km s−1,the second local maximum is atθ=12◦:v max=850km s−1. The maximum velocity gradually decreases towards higher inclinations v max(θ=27◦)= 343km s−1;and atθ=60◦it is v max=110km s−1.Closer to black hole,at about0.2pc,the vθcomponent of the velocity is more pronounced,until heights z 1.4pc are reached forming a base of the evaporative wind.After this time,theflow is approximately symmetrical in both hemispheres.Because we are solving equations of ideal hydrodynamics(with only a small numerical viscosity),accretion through inner boundary(at r=0)is almost negligible:˙M in (M yr−1)<10−8.The mass-loss rate˙M maxΩ(M yr−1sterrad−1)peaks atθ 10◦,i.e.atmuch higher inclinations than v max.The total mass-loss rate at this stage is˙M(M yr−1) 3·10−4.Figure1shows theflow streamlines and density contours at three orbital periods.Atthis time the high pressure region expands vertically,to z 10pc from the inner torus.The torus inner edge can be inferred from the temperature and density maps: − 1.3pc.Inside a throat of this torus,T 10T vir.The contours of T become moreflattened:z max 4pc, + 8pc.The conservation of angular momentum helps to keep the outer edge of the torus at∼5pc.However,there is an envelope around this dense torus:z max 4pc, + 8.1pc. The values of the minimum ionization parameter and the column density vary significantly with the inclination angle:ξmin(θ=8◦)=2000,N22=0.3;atθ 25◦,the ionization parameter decreases significantly:ξmin(θ=26◦)=63,N22=2.3;and at higher inclination, the ionization parameter is quite low:ξmin(θ=53◦)=6.6,and the obscuration is quite high:N22=75.The mass loss rate changes slowly d˙M/dt((M yr−1)/yr) 1.53·10−6.The mass-loss rate peaks at˙M maxΩ=0.05atθ 20◦,where v max(θ=20◦)=616km s−1;the maximum value of v max(θ=5◦)=1000km s−1;The total mass-loss rate is˙M(M yr−1) 0.08.It is this evolved model that gives mass-loss rate in accord with the estimates of (Krolik&Begelman1986).Figure2shows theflow atfive orbital periods.At this time the density maximum is at =3.6.Remarkably,the inner edge of the inner,dense torus is at the same distance from the black hole: − 1.3pc,as it was at three orbital periods,while the outer edge is at + 6.2pc.The position of the outer edge of the torus,as infered from the temperature maps,extends to11pc.Outside this region theflow temperature is T 2.5T vir.The significant drop of ionization parameterξfrom∼103to∼10,occurs again atθ=25◦,where the column also rises to a∼1022.Aspect ratio of the torus:∆r/r∼1in accord with what is inferred from observations(Krolik&Begelman1986;Jaffe et al.2004).Almost everywhere in the wind the poloidal component of the velocity is determmined by v r.However,closer to the black hole,the vθcomponent is important,vθ∼v r.The mass-loss rate is approximatelyconstant at15◦<θ<60◦:˙M maxΩ=0.07,and has a peak atθ=74◦:˙M maxΩ=0.16.The totalmass-loss rate is˙M(M yr−1) 0.25and d˙M/dt((M yr−1)/yr) 10−6.The maximum value of v max(θ=3◦)=1032km s−1;another local peak is atθ=15◦,where the maximum velocity is v max=606km s−1,and the minimum v max(θ=90◦)=180km s−1.The torus is losing mass in all directions,although with very different speed at different inclinations.We have performed multidimensional simulations of a wind excited by X-ray heating of a rotationally supported torus.Our dynamical calculations predict the velocityfield and the spatial distribution of opacity and emissivity of the gas in both continuum and lines as a function of position.(Synthesizing the spectrum provides a key test for our model).We have calculated synthetic spectra by integrating over the wind and using the formal solution of the transfer equation.This is done by passing the results of the hydrodynamical calculations into a code which calls the subroutines from the xstar code(Kallman&Bautista2001) to calculate the transmittedflux.In this paper we present only absorption spectra.Thisapproximately represents the case when warm absorber gas lies on the line of sight to the observer and we see only transmitted spectra.These are shown in Figure3,for various anglesθ=26◦,35◦,44◦at three orbital periods.These show that our simulations provide gas with intermediate ionization and sufficient column to produce observable warm absorber features.This supports the idea that it is this wind that is responsible for the warm absorber gas observed in Seyfert galaxies.More detailed results,including dependence of these results on different parameters as well as limitations of the adopted model and comparisons with observations,will be discussed in a separate paper.This research was supported by an appointment to the NASA Postdoctoral Program at the NASA Goddard Space Flight Center,administered by Oak Ridge Associated Universities through a contract with NASA,and by grants from the NASA Astrophysics Theory Program 05-ATP05-18.REFERENCESAntonucci,R.R.J.,Miller,J.S.ApJ,297,621Balsara,D.S.,Krolik,J.1992,ApJ,402,109Blondin,J.M.1994,ApJ,435,756Basko,M.M.,Hatchett,S.,McCray,R.,Sunyaev,R.A.1977,ApJ,215,276Behar,E.,Rasmussen,A.P.,Blustin,A.J.,et al2003,ApJ,598,232Castor,J.I.,Abbott,D.C,Klein,R.1975,ApJ,195,157Chelouche,D.,Netzer,H.2005,ApJ,625,95Crenshaw,D.M.,et al.1999,ApJ,516,750Chartas,G.,Brandt,W.N.,Gallagher,S.C.,Garmire,G.P.2002,ApJ,279,169 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carry information about the direction only i.e.the magnitude of the velocity at low inclination is much higher than near the equatorial plane.orbital periods;at northern hemisphere superimposed with velocity vectors.Fig. 3.—The transmitted spectra observed at three orbital periods from2.5D model of the evaporative torus wind.Each panel corresponds to a different viewing angle,θ=26◦,35◦,44◦;x-axis:energy;y-axis:normalized,transmittedflux.The initial spec-trum is a power law with energy indexα=1.。

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